Device and method for thermal cycling

ABSTRACT

A thermal cycling device for performing nucleic acid amplification on a plurality of biological samples positioned in a sample well tray. The thermal cycling device includes a sample block assembly, an optical detection system, and a sample well tray holder configured to hold the sample well tray. The sample block assembly is adapted for translation between a first position permitting the movement of the sample well tray into alignment with sample block assembly, and a second position, upward relative to the first position, where the sample block assembly contacts the sample well tray. A method of performing nucleic acid amplification on a plurality of biological samples positioned in a sample well tray in a thermal cycling device is also provided.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.12/406,711 filed Mar. 18, 2009 now abandoned, which was a continuationof U.S. application Ser. No. 10/756,219 filed Jan. 12,2004 nowabandoned, which was a continuation of U.S. application Ser. No.10/058,927 filed Jan. 30, 2002 now U.S. Pat. No. 6,677,151, all of whichare incorporated herein by reference.

FIELD

The present invention relates generally to a thermal cycling device andmethod of performing nucleic acid amplification on a plurality ofbiological samples positioned in a sample well tray. More particularly,the present invention relates in one aspect to a thermal cycling deviceand method of real-time detection of a nucleic acid amplificationprocess such as polymerase chain reaction (PCR).

BACKGROUND

Biological testing has become an important tool in detecting andmonitoring diseases. In the biological testing field, thermal cycling isused to amplify nucleic acids by, for example, performing PCR and otherreactions. PCR in particular has become a valuable research tool withapplications such as cloning, analysis of genetic expression, DNAsequencing, and drug discovery.

Recent developments in the field have spurred growth in the number oftests that are performed. One method for increasing the throughput ofsuch biological testing is to provide real-time detection capabilityduring thermal cycling. Real-time detection increases the efficiency ofthe biological testing because the characteristics of the samples can bedetected while the sample well tray remains positioned in the thermalcycling device, therefore not requiring removal of the sample well trayto a separate area prior to testing of the samples. In typical real-timethermal cycling devices, the sample well tray is removed after detectionis completed.

SUMMARY

Various aspects of the invention generally relate to a thermal cyclingdevice in which the sample block assembly may be vertically moved sothat the sample well tray may be inserted and removed from the thermalcycling device. The thermal cycling device can be a real-time device.During such movement of the sample block assembly and sample well tray,the optical detection system can remain substantially stationary.

According to one aspect, the invention comprises a thermal cyclingdevice. The thermal cycling device includes a sample block assembly, anoptical detection system, and a sample well tray holder. The sample welltray holder includes a tray-receiving region configured to hold a samplewell tray. The optical detection system is positioned above the sampleblock assembly. The sample well tray holder is configured to translatethe sample well tray into alignment with the sample block assembly. Thesample block assembly is adapted for movement between a first positionpermitting the translation of the sample well tray into alignment withthe sample block assembly, and a second position, upward relative to thefirst position, where the sample block assembly contacts the sample welltray.

In another aspect, the optical detection system is adapted to remainsubstantially stationary during insertion and removal of the sample welltray from the thermal cycling device. In a further aspect, the thermalcycling device further includes a positioning mechanism configured totranslate the sample block between the first and second positions.

In yet another aspect, the invention comprises a method of performingnucleic acid amplification on a plurality of biological samplespositioned in a sample well tray in a thermal cycling device. The methodincludes the step of placing the sample well tray into a sample welltray holder. The method further includes the step of translating thesample well tray holder and sample well tray into the thermal cyclingdevice until the sample well tray is aligned with a sample blockassembly positioned beneath the sample well tray. The method furtherincludes the step of translating the sample block assembly from a firstposition to a second position. In the first position, the sample blockassembly permits the sample well tray to translate into alignment withthe sample block assembly. In the second position, the sample blockassembly is positioned vertically upward relative to the first positionto contact the sample well tray.

The method can further comprise the step of thermally cycling the devicewhile simultaneously optically detecting the samples. The method canfurther comprise translating the sample block assembly from the secondposition to the first position. Finally, the method can comprise thestep of removing the sample well tray holder and sample well tray fromthe thermal cycling device. In various embodiments, the opticaldetection system remains substantially stationary throughout the abovesteps.

In another aspect, the invention comprises a thermal cycling device. Thethermal cycling device includes an optical detection system, a sampleblock, and a sample well tray holder. The sample block is adapted formovement along a first path, toward and away from the optical detectionsystem. The sample well tray holder includes a tray-receiving region.The sample well tray holder is adapted for movement along a second path,toward and away from a position whereat the tray-receiving region isdisposed between the optical detection system and the sample block. Theoptical detection system can be adapted to remain substantiallystationary during movement of the sample block and the sample well trayholder along the first and second paths.

It is to be understood that both the foregoing general description andthe following detailed description are exemplary and explanatory onlyand are not restrictive of the invention, as claimed.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings, which are incorporated in and constitute apart of this specification, illustrate several embodiments of theinvention. In the drawings,

FIG. 1 is a front view of an exemplary embodiment of a thermal cyclingdevice according to the present invention;

FIG. 2A is side view of an embodiment of the device of FIG. 1, with asample well tray positioned outside of the device;

FIG. 2B is a side view of the device of FIG. 1, with the sample welltray inserted into the device;

FIG. 2C is a side view of the device of FIG. 1, with the sample welltray inserted into the device and a sample block assembly in an upwardposition for engaging the sample well tray;

FIG. 3A is a side view of another embodiment of the thermal cyclingdevice of the invention, with a sample well tray positioned outside ofthe device;

FIG. 3B is a side view of the device of FIG. 3A, with the sample welltray inserted into the device;

FIG. 3C is a side view of the device of FIG. 3A, with the sample welltray inserted into the device and a sample block assembly in an upwardposition for engaging the sample well tray;

FIG. 4A is side view of yet another embodiment of the thermal cyclingdevice of the invention, with the sample well tray positioned outside ofthe device;

FIG. 4B is a side view of the device of FIG. 4A, with the sample welltray inserted into the device;

FIG. 4C is a side view of the device of FIG. 4A, with the sample welltray inserted into the device and a sample block assembly in an upwardposition for engaging the sample well tray;

FIG. 5 is a side cross sectional view of a sample well tray holder, usedwith the present invention, with a sample well tray positioned thereon;and

FIG. 6 is a perspective view of one embodiment of a sample blockassembly used in the device of the invention.

DETAILED DESCRIPTION

Reference will now be made to certain exemplary embodiments of theinvention, examples of which are illustrated in the accompanyingdrawings. Wherever possible, the same reference numbers are used in thedrawings and the description to refer to the same or like parts.

In accordance with certain embodiments, a thermal cycling device isprovided. In one aspect, the thermal cycling device may perform nucleicacid amplification on a plurality of biological samples positioned in asample well tray. In certain embodiments, the thermal cycling deviceincludes a sample block assembly, an optical detection system positionedabove the sample block assembly, and a sample well tray holder with atray-receiving region configured to hold the sample well tray. Incertain aspects, the sample block assembly is adapted for movementbetween a first position permitting the translation of the sample welltray into alignment with the sample block assembly, and a secondposition, upward relative to the first position, where the sample blockassembly contacts the sample well tray. The thermal cycling device mayalso include a positioning mechanism for translating the sample blockbetween the first and second positions.

Although the terms “horizontal,” “vertical,” “upward,” and “downward”are used in describing various aspects of the present invention, itshould be understood that such terms are for purposes more easilydescribing the invention, and do not limit the scope of the invention.

In various embodiments, such as illustrated in FIGS. 1, 2A-2C, and 5-6,the thermal cycling device 10 for performing nucleic acid amplificationon a plurality of biological samples includes one or more of: a sampleblock assembly 50; an optical detection system 12 for detecting thecharacteristics of the samples positioned in a sample well tray 14; asample well tray holder 30; and a positioning mechanism 70 connected tothe sample block assembly, the positioning mechanism being configured toimpart vertical movement on the sample block assembly.

The thermal cycling device is typically configured to perform nucleicacid amplification. One common method of performing nucleic acidamplification of biological samples is polymerase chain reaction (PCR).Various PCR methods are known in the art, as described in, for example,U.S. Pat. Nos. 5,928,907 and 6,015,674 to Woudenberg et al., thecomplete disclosures of which are hereby incorporated by reference forany purpose. Other methods of nucleic acid amplification include, forexample, ligase chain reaction, oligonucleotide litigations assay, andhybridization assay. These and other methods are described in greaterdetail in U.S. Pat. Nos. 5,928,907 and 6,015,674.

In one embodiment, the thermal cycling device performs real-timedetection of the nucleic acid amplification of the samples duringthermal cycling. Real-time detection systems are known in the art, asalso described in greater detail in, for example, U.S. Pat. Nos.5,928,907 and 6,015,674 to Woudenberg et al., incorporated herein above.During real-time detection, various characteristics of the samples aredetected during the thermal cycling in a manner known in the art.Real-time detection permits more accurate and efficient detection andmonitoring of the samples during the nucleic acid amplification.

In accordance with various embodiments, the thermal cycling deviceincludes an optical detection system. As embodied herein and shown inFIGS. 1 and 2A-2C, an optical detection system 12 is positioned abovethe sample block assembly 50. The optical detection system 12 isconfigured to detect and monitor the characteristics of the samples inthe sample well tray 14 in real-time during the thermal cycling.Suitable structures and methods for the optical detection system 12 arewell known in the art. The optical detection system may use any knownstructure or method. In one example, the optical detection system wouldinclude a quartz bulb with a CCD camera, in a manner known in the art.In another example, the optical detection system may include afluorescence based system with a lens and a fiber optics for each cableas described in U.S. Pat. Nos. 5,928,907 and 6,015,674 to Woudenberg etal, incorporated herein above. Alternatively, the optical detectionsystem may include any known system using a single light source for eachsample well, in a manner known in the art. Likewise, the opticaldetection system may include any other type suitable for use with thethermal cycling device of the present invention.

In various embodiments, optical detection system 12 is substantiallystationarily mounted in the thermal cycling device. The opticaldetection system can be configured so that the optical detection systemremains substantially stationary during insertion of a sample well trayholder and sample well tray into the thermal cycling device, duringthermal cycling of the sample well tray, during removal of the samplewell tray holder and sample well tray from the thermal cycling device,and at all stages in between the above steps. By remaining substantiallystationary, the optical system reduces the potential for misalignment ofthe optical components. For purposes of this invention, the term“substantially stationary” does not mean that the optical detectionsystem is completely stationary, rather, the term includes anyvibrations or movements caused by normal operation of the thermalcycling device.

The thermal cycling device may be configured for use with any type ofsample well tray, including, for example, 96-well sample well trays,384-well sample trays, and microcard sample trays. The size and shape ofthese sample well trays are well known in the art. Examples of 96-wellsample well trays suitable for use in the present invention aredescribed in WO 00/25922 to Moring et al., the complete disclosure ofwhich is hereby incorporated by reference for any purpose. Examples ofsample well trays of the microcard type suitable for use in the presentinvention are described in WO 01/28684 to Frye et al., the completedisclosure of which is hereby incorporated by reference for any purpose,WO97/36681 to Woudenberg et al., the complete disclosure of which ishereby incorporated by reference for any purpose, U.S. application Ser.No. 09/897,500, filed Jul. 3, 2001, assigned to the assignee of thepresent invention, the complete disclosure of which is herebyincorporated by reference for any purpose, and U.S. application Ser. No.09/977,225, filed Oct. 16, 2001, assigned to the assignee of the presentapplication, the complete disclosure of which is hereby incorporated byreference for any purpose. Sample well trays having any number of samplewells and sample well sizes may also be used with the thermal cyclingdevice of the present invention. In the example shown in the figures,the volume of the sample wells may vary anywhere from about 0.01:l tothousands of microliters (:l), with a volume between 10 to 500:l beingtypical.

As embodied herein and shown in FIGS. 1, 2A-2C, and 5, the sample welltray 14 can include a rectangular top portion 16 having a top surface 18and bottom surface 24. The top surface 18 defines openings for aplurality of sample wells 20 of any known size and shape. In the exampleshown in FIGS. 1-6, the sample well tray includes ninety-six samplewells positioned in a well-known 8×12 array. In the embodiment shown,the top portion 16 of the sample well tray is rectangular. In theembodiment shown in the figures, the sample wells are conical shaperecesses extending downwardly from the top surface 18 in a known manner.Each sample well includes a sample well bottom surface 22 for engagingwith corresponding recesses in the sample block assembly 50. It is wellunderstood that any type of sample well configuration may be used withthe present invention, including for example, a 384-well sample welltray and a microcard type sample tray.

In accordance with various embodiments, the thermal cycling device caninclude a sample well tray holder having a tray-receiving regionconfigured to hold the sample well tray. The sample well tray holder canbe configured to translate the sample well tray into alignment with asample block assembly. As described herein and shown in FIGS. 1, 2A-2C,and 5, the sample well tray holder is generally designated by referencenumber 30. The sample well tray holder is configured so that the samplewell tray may be supported thereon, particularly during insertion of thesample well tray into the thermal cycling device, and during removal ofthe sample well tray from the thermal cycling device. In variousembodiments, the sample well tray holder 30 is generally rectangular inshape.

With particular reference to FIG. 5, the sample well tray holder 30includes a top surface 32 and a side surface 34 that extends around theperiphery of the sample well tray holder. The side surface in the frontof the device is designated by reference number 36. The sample well trayholder further includes a tray-receiving region configured to hold asample well tray. In the embodiment shown in FIG. 5, the tray-receivingregion is defined by a downwardly projecting holder structure 38 in thetop surface 32. The downwardly projecting holder structure 38 ispositioned on a first recessed portion 40 of the top surface 32. Thedownwardly projecting holder structure 38 includes a horizontallyprojecting annular projection 42 for engaging the top surface of thefirst recessed portion 40 of the top surface 32. The downwardlyprojecting holder structure 38 further comprises a projection 44 thatslopes inwardly. The inside of the projection 44 defines a rectangularopening or recess slightly smaller than the sample well tray 16. Therectangular opening or recess is dimensioned to receive a sample welltray. In particular, the projection 44 is dimensioned so that the bottomsurface 24 of the sample well tray may rest on the top surface of theprojection 44, as shown in FIG. 5. The projecting holder structure maybe shaped to be angled inwardly in order to ease the removal of thesample well tray from the sample well tray holder.

The sample well tray holder 30 and sample well tray 14 are dimensionedso that they are capable of passing between the optical detection system12 and the sample block assembly 50 without interference duringinsertion into and removal from the thermal cycling device. The samplewell tray is configured so that it can horizontally translate into andout of the thermal cycling device on the sample well tray holder. Inorder to facilitate insertion or removal of the sample well tray holder,bearing surfaces (not shown) may be provided on the sample well trayholder and/or thermal cycling device. The sample well tray holder may behorizontally translated either manually or automatically.

In accordance with various embodiments, the thermal cycling device caninclude a sample block assembly configured to receive the sample welltray thereon. As described herein and shown in FIGS. 1, 2A-2C, 5, and 6,a sample block assembly is generally designated by reference number 50.It is to be understood that the sample block assembly shown in FIG. 6 isby way of example only, and the invention is not limited to the sampleblock assembly shown in FIG. 6. The sample block assembly shown in FIG.6 includes a sample block 58 and a heat sink 56. Sample blocks are wellknown in the art. Sample blocks may be made of any suitable material,such as aluminum. The sample block assembly typically includes at leastone heating element. In one embodiment, the at least one heating elementincludes a peltier heater. Methods of heating and cooling a sample blockduring and after thermal cycling are known in the art. The sample block58 shown in FIG. 6 includes a top surface 54 with a plurality of recess52 on the top surface. The recesses are arranged to correspond to thesample wells of the sample well tray. For example, in the embodimentshown in FIG. 6, the sample block assembly includes ninety-six recessesfor engaging with a 96-well sample well tray. Alternatively, the sampleblock assembly can have any number of recesses. For example, the numberof recesses can equal the number of sample wells. In an embodiment witha 384-well sample tray, the sample block assembly would typically haveat least 384 recesses. In an embodiment using a microcard type sampletray, the sample block need not have recesses.

Heat sink 56 may be any known type of heat sink. Additionally, aconvection unit such as a fan may be positioned adjacent the sampleblock assembly. In the embodiment shown in FIGS. 1, 2A-2C, and 5-6, theconvection unit comprises a fan 66 positioned below the sample blockassembly 50. In one embodiment, the fan 66 creates a flow of cooling airagainst the heat sink 56 in order to cool the sample block.Alternatively, the fan may be used with a heater in order to create aflow of hot air against the heat sink in order to heat the sample block.In certain embodiments, the fan is mounted so that it moves verticallywith the sample block assembly. In other embodiments, the fan may bestationarily mounted in the thermal cycling device

In accordance with various embodiments, the thermal cycling device caninclude a positioning mechanism connected to the sample block assembly,the positioning mechanism being configured to vertically translate thesample block assembly between a first or “downward” position and asecond or “upward” position. The positioning mechanism can be configuredto translate the sample block assembly between the first position, wherethe sample block assembly permits the translation of the sample welltray into alignment with the sample block assembly, and the secondposition, upward relative to the first position, where the sample blockassembly contacts the sample well tray.

An embodiment of the positioning mechanism is illustrated in FIGS. 1 and2A-2C. In the embodiment shown in FIGS. 1 and 2A-2C, the positioningmechanism is generally designated by reference number 70. Thepositioning mechanism is connected to the sample block assembly 50. Thepositioning mechanism allows insertion and removal of the sample welltray by moving the sample block assembly in the vertical direction.FIGS. 2A and 2B show the downward or “first” position of the sampleblock assembly. In the downward position, a gap is created between thetop of the sample block assembly 50 and a bottom portion 94 of theoptical detection system of sufficient size so that the sample well trayholder and sample well tray may be inserted therebetween. In the firstposition, the sample block is “away” from the optical detection system.

In a second or “upward” position shown in FIG. 2C, the sample blockassembly 50 is vertically upward relative to the downward or “first”position. In the upward position, the top surface 54 of the sample block58 presses against the bottom of the sample well tray 14 so that therecesses 52 mate with the sample well bottom surfaces 22. In variousembodiments using a microcard, a top surface of the sample block canpress against a bottom surface of the microcard. In the second position,the sample block is “toward” the optical detection system. The sampleblock assembly is adapted for movement toward and away from the opticaldetection system along a predetermined vertical path.

In the embodiment shown in FIGS. 1 and 2A-2C, the positioning mechanism70 includes a plurality of links. The arrangement of links shown inFIGS. 1 and 2A-2C is by way of example only. The plurality of linksincludes a first link 78 as shown in FIGS. 2A-2C. The first link 78 isshown as being in the shape of a connecting rod, however, the first linkmay have any number of different shapes. First link 78 includes a firstend 80 rotatably connected to a motor 72 at a pivot point 74. Motor 72can be any known type of motor that is capable of imparting atranslational or rotational force on the first link 78. As shown inFIGS. 2A-2C, the motor causes pivot point 74 of the first end 80 torevolve around a central axis 76 of the motor. The revolution of thefirst end 80 about the central axis of the motor causes the first linkto translate.

As shown in FIGS. 2A-2C, a second end 82 of the first link is rotatablyconnected to a first end of a second link 84 at pivot point 88. Thesecond link has a second end rotatably connected to stationary pivotpoint 86. The second link 84 pivots about stationary pivot point 86 whenthe motor causes movement of the first link 78.

The second end 82 of the first link is rotatably connected to a firstend of a third link 90 at pivot point 88. The second end of the thirdlink 90 is rotatably connected to the sample block assembly at pivotpoint 92. By revolution of the first end of the first link about thecentral axis 76 of the motor, the first link causes the first end of thesecond link 84 to rotate partially about the stationary pivot point 86,thus causing the third link to press upward against the sample blockassembly at pivot point 92. The positioning mechanism is connected tothe sample block assembly by, for example, a pin at pivot point 92. As aresult of this linkage arrangement, the positioning mechanism causes thesample block assembly to move vertically from the downward or “first”position shown in FIGS. 2A and 2B to the upward or “second” positionshown in FIG. 2C. It should be understood that the positioning mechanismof FIGS. 2A-2C is by way of example only.

As shown in FIG. 1, the positioning mechanism 70 may include two sets oflinks, one on each lateral side of the sample block assembly. The secondset of links is a mirror image of the first set of links. In FIG. 1, thesecond set of links includes first link (not shown), second link 84′,and third link 90′. With a configuration having two sets of links, anindividual motor may be utilized for each of the sets of links, oralternatively, a single motor may be utilized for both sets of links. Inanother variation, a single set of links may be used instead of two setsof links. In a further variation, more than two sets of links may beused.

The positioning mechanism may also include at least one guide member forguiding the sample block assembly in the vertical direction. The guidemember can be configured to prevent the sample block assembly frommoving in the horizontal direction. Any known type of guide member maybe utilized. In the embodiment shown in FIGS. 1 and 2A-2C, the guidemember includes a plurality of vertical shafts 96 fixedly attached tothe lateral sides of the sample block assembly 50. As shown in FIG. 1,the vertical shafts are positioned on each lateral side of the samplewell tray holder 30 and sample well tray 14. Each vertical shaft 96 isreceived within bearing member 98. Bearing member is stationarilymounted adjacent the optical detection system. Each vertical shaft 96slides within a corresponding cylindrical opening in the bearing member98. The bearing members 98 and vertical shafts 96 may include any typeof known bearing arrangement.

Alternatively, in another variation, the vertical shaft could bestationarily fixed to the thermal cycling device so that the sampleblock assembly translates vertically relative to the vertical shaft.With such an arrangement, the bearing structures would be mounted withincylindrical openings in the sample block assembly for receiving thevertical shafts.

The guide member may be any other type of known guide member capable oflimiting movement of the sample block assembly in the horizontaldirection as the sample block assembly is moved in the verticaldirection. For example, the guide member could include any type ofvertical guiding structure adjacent the sample block assembly. It shouldbe understood that the guide member shown in FIGS. 2A-2C is by way ofexample only.

An operation of the thermal cycling device for the embodiment of FIGS. 1and 2A-2C is further described below. First, with the sample well trayholder 30 in an outward position as shown in FIG. 2A, a sample well tray14 is placed in the sample well tray holder. The sample well tray can bedropped into the recess defined by downwardly projecting holderstructure 38 shown in FIG. 5. The sample well tray 14 may be placed inthe sample well tray holder 30 either manually or robotically.

In FIG. 2A, the sample block assembly 50 is in a downward or “first”position so that a gap is created between the optical detection system12 and the uppermost surface of the sample block 58. The gap that iscreated is larger than the vertical dimension of the sample well trayholder 30 and sample well tray 14.

After the sample well tray 14 is placed in the sample well tray holder30, the sample well tray holder is horizontally translated into thethermal cycling device 10 until the sample well tray reaches a positionwhere the sample wells of the sample well tray align with the recesses52 of the sample block 58. The horizontal translation may be caused byan operator or a robot pressing on the sample well tray. In theembodiment shown in FIGS. 1 and 2A-2C, the sample well tray holder 30can be horizontally translated until each of the ninety-six sample wellsalign with a corresponding recess 52 in the sample block 58. FIG. 2Bshows the sample well tray holder 30 and sample well tray 14 in theposition where the sample wells 20 are aligned with correspondingrecesses in the sample block 58. As shown in FIG. 2B, the sample blockassembly 50 can remain in the downward position until the sample welltray is fully inserted into the thermal cycling device and aligned.

After the sample well tray 14 has been fully inserted into the thermalcycling device 10 and proper alignment has been achieved between thesample wells 20 and the recesses 52 of the sample block (as shown inFIG. 2B), the motor 72 can be actuated to begin a revolution of thefirst end 80 of the first link 78. As the first end 80 of the first link78 begins to revolve around the central axis 76 of the motor, the pivotpoint 88 is moved leftward as shown in FIG. 2C, and the pivot point 92of the second end of the third link imparts an upward force on thesample block assembly 50. As a result, the sample block assembly 50 ismoved upward so that the top surface 54 of the sample block firmlycontacts the bottom surface of the sample well tray 14. In the upwardposition (also referred to as the “second position”) shown in FIG. 2C,the sample block assembly 50 is firmly positioned against the samplewell tray 14 so that the sample wells 22 are seated against the sampleblock. The thermal cycling device 10 is now ready for thermal cyclingprocesses.

At any desired time, e.g., after the thermal cycling processes arecompleted, the sample well tray 14 can be removed by actuating the motorso that the sample block assembly 50 moves to a downward position (asshown in FIG. 2B), and then horizontally translating the sample welltray holder 30 and sample well tray 14 to the position shown in FIG. 2A.The sample well tray 14 may then be removed from the sample well trayholder 30.

The amount of vertical displacement of the sample block assembly 50between the downward (“first”) and upward (“second”) positions dependson the specific application, the type and size of sample well tray thatis utilized, and other practical concerns. For example, in anapplication for use with a 96-well sample well tray, the amount ofvertical displacement would typically be between about 0.5 to 1.5inches, but it could be much greater or much less. In an applicationwith a 384-well sample tray having smaller sample wells, or a microcard,the amount of vertical displacement of the sample block assembly may beless. For practical purposes however, it may also be desirable tovertically displace the sample block assembly a much greater distance inorder to provide better access to the inside of the device forinspection or maintenance.

In accordance with various embodiments, the optical detection system 12can be mounted in a substantially stationary manner in the thermalcycling device during insertion and removal of the sample well tray toand from the thermal cycling device, during thermal cycling, and duringall steps therebetween.

In accordance with further various embodiments of the positioningmechanism, the plurality of links comprises a first link and a secondlink. The first link has a first end rotatably connected to a stationarypivot point. The first link also has a second end comprising a handlefor manual manipulation of the first link. The second link has a firstend rotatably connected to a pivot point on the first link. The secondlink also has a second end rotatably connected to the sample blockassembly.

Further various embodiments of the sample block assembly positioningmechanism contemplate structure such as shown in FIGS. 3A-3C. Thepositioning mechanism is generally designated by the reference number100 in FIGS. 3A-3C. The positioning mechanism includes a plurality oflinks such as first link 102 and second link 104. As shown in FIG. 3A,the first link 102 has a first end rotatably connected to a stationarypivot point 106 and a second end defining a handle 108 for manualmanipulation of the first link. In FIGS. 3A-3C, the first link 102 is inthe shape of a connecting rod with a bend as shown in FIG. 3A. Thehandle 108 of the first link 102 defines a door 112 corresponding to anopening 114 in the thermal cycling device. The door 112 is configured tocover the opening 114 in the thermal cycling device when the handle isactuated in a manner described below. Although the door is shown havingan arcuate shape on the inner surface, any other suitable shape is alsoacceptable.

As shown in FIG. 3A, the second link 104 has a first end rotatablyconnected to a pivot point 118 positioned on first link 102. The secondlink 104 has a second end rotatably connected to the sample blockassembly 50 at pivot point 120. By the linkage arrangement describedabove, the actuation of the handle 108 will cause the sample blockassembly 50 to translate in the vertical direction.

An operation of the thermal cycling device for the embodiment of FIGS.3A-3C will be briefly described below. To the extent that the followingoperation is similar to the operation described above for the embodimentshown in FIGS. 1 and 2A-2C, a detailed description of the operation willnot be repeated. Moreover, the same reference numbers will be used torefer to the same or like parts as shown in the embodiment of FIGS. 1and 2A-2C. FIG. 3A shows the sample well tray holder 30 and sample welltray 14 in an outward position. In FIG. 3A, the sample block assembly 50is in the downward or “first” position. The sample well tray holder 30is then inserted into the thermal cycling device 10 by translating inthe horizontal direction until the sample well tray 14 reaches itsproper aligned position (shown in FIG. 3B) between the optical detectionsystem and the sample block assembly.

After the sample well tray 14 reaches its aligned position, an operatormay manually press against the handle 108 to rotate the first link 102about the stationary pivot point 106. In another embodiment, the handlemay be rotated robotically. In either case, the clockwise rotation (inreference to FIGS. 3A-3C) of the first link 102 results in the pivotpoint 118 moving upward, thereby causing the pivot point 120 on thesecond link 104 to move upward. The upward movement of the second linkresults in translation of the sample block assembly 50 in an upwardvertical direction to an upward or “second” position (shown in FIG. 3C).The positioning mechanism is configured so that the door 112 is fullyclosed as shown in FIG. 3C when the top surface of the sample blockfirmly contacts the sample well tray. When the sample block assembly isin the upward position, as shown in FIG. 3C, the thermal cycling deviceis ready for thermal cycling processes.

At any desired time, e.g., upon completion of the thermal cyclingprocesses, the handle 108 may be rotated counterclockwise, therebytranslating the sample block assembly 50 back to the downward positionshown in FIG. 3B. The sample well tray holder can then be slid from thethermal cycling device and returned to the position shown in FIG. 3A,and the sample well tray 14 may be removed from the sample well trayholder.

In accordance with still further embodiments of the positioningmechanism, the plurality of links can comprise a first link and a secondlink. The first link is rotatably connected to a stationary pivot point.The first link has a first end rotatably connected to the second linkand a second end comprising a handle for manual manipulation of thefirst link. The second link has a first end rotatably connected to thefirst end of the first link and a second end rotatably connected to thesample block assembly.

Such embodiments of the positioning mechanism include that shown inFIGS. 4A-4C. As shown in FIGS. 4A-4C, the positioning mechanism isgenerally designated by reference number 130. The positioning mechanism130 includes a plurality of links such as first link 132 and second link134. As shown in FIG. 4A-4C, the first link 132 is rotatably connectedto a stationary pivot point 136. The first link 132 has a first endrotatably connected to the second link 134 at a pivot point 138. Thefirst link includes a second end comprising a handle 140 for manual orautomatic manipulation of the first link 132. The second link 134includes a first end rotatably connected to the first end of the firstlink at pivot point 138. The second link 134 further includes a secondend rotatably connected to the sample block assembly 50 at pivot point142.

As shown in FIGS. 4A-4C, the first link 132 includes a first segment 144and a second segment 146. In FIGS. 4A-4C, the first segment 144 andsecond segment 146 of the first link are substantially perpendicular toeach other. This angle is by way of example only, as the linkages mayhave various configurations. By the linkage arrangement described above,the actuation of the handle 140 will cause the sample block assembly totranslate in the vertical direction.

An operation of the thermal cycling device for the positioning mechanismof FIGS. 4A-4C will be briefly described below. To the extent that thefollowing operation is similar to the operation for the otherembodiments described above, a detailed description of the operationwill not be repeated. FIG. 4A shows the sample well tray holder 30 andsample well tray 14 in an outward position. In FIG. 4A, the sample blockassembly 50 is in the downward or “first” position. The sample well trayholder 30 is then inserted into the thermal cycling device 10 bytranslating in the horizontal direction until the sample well trayreaches its proper aligned position (shown in FIG. 4B).

After the sample well tray reaches its aligned position, an operator maymanually or automatically press downward against the handle 140 torotate the first link 132 about the stationary pivot point 136 in acounterclockwise direction (in reference to FIGS. 4A-4C). Thiscounterclockwise rotation of the first link 132 results in the pivotpoint 138 moving upwardly thereby causing the second link 134 to moveupwardly. The upward movement of the second link results in translationof the sample block assembly 50 in an upward vertical direction to anupward or “second” position. FIG. 4C shows the sample block assembly inthe upward or “second” position. When the sample block assembly is inthe upward position, as shown in FIG. 4C, the thermal cycling device isready for thermal cycling processes.

At any desired time, e.g., upon completion of the thermal cyclingprocesses, the handle 104 may be rotated clockwise, thereby translatingthe sample block assembly 50 back to the downward position as shown inFIG. 4B. The sample well tray holder 30 can then be slid from thethermal cycling device and returned to the position shown in FIG. 4A,and the sample well tray 14 may be removed from the sample well trayholder.

The sample block assembly positioning mechanisms shown in the figuresare provided for purposes of example only. Other positioning mechanismscould be, for example, a hydraulic, a spring, a lever, a cam, asolenoid, or any other suitable motion-producing device.

As is clear from the above description, the present invention includes amethod of performing nucleic acid amplification on a plurality ofbiological samples positioned in a sample well tray in a thermal cyclingdevice. The method includes the step of placing the sample well trayinto a sample well tray holder. The sample well tray 14 shown in thefigures is configured for placement into a corresponding recess in thesample well tray holder 30.

The method further includes the step of translating the sample well trayholder and sample well tray into the thermal cycling device until thesample well tray is aligned with a sample block assembly positionedbeneath the sample well tray. In one aspect, the translation of thesample well tray holder is in the horizontal direction. The alignedposition is shown for example in FIG. 2B. The method further includesthe step of translating the sample block assembly from a first positionto a second position. In one aspect, the translation of the sample blockassembly is in the vertical direction. In the first position, the sampleblock assembly permits the sample well tray to translate into alignmentwith the sample block assembly. The first position of the sample blockassembly 50 is shown for example in FIG. 2B. In the second position, thesample block assembly is positioned vertically upward relative to thefirst position in order to contact the sample block assembly to thesample well tray. The second position of the sample block assembly 50 isshown for example in FIG. 2C.

The method further comprises thermally cycling the device whilesimultaneously optically detecting the samples. An optical detectionsystem 12 is positioned within the thermal cycling device 10 fordetecting the characteristics of the sample. The method furthercomprises translating the sample block assembly from the second positionto the first position. Finally, the method comprises the step ofremoving the sample well tray from the thermal cycling device. Theoptical detection system remains substantially stationary throughout theabove steps.

It is clear that the present invention is not limited to the examplesshown. For example, a thermal cycling device could be configured tohandle several sample well trays, e.g., positioned side by side. Such anarrangement could include a corresponding optical system and sampleblock.

It will be apparent to those skilled in the art that variousmodifications and variations can be made to the structure. Thus, itshould be understood that the invention is not limited to the examplesdiscussed in the specification. Rather, the present invention isintended to cover modifications and variations.

What is claimed is:
 1. A method of performing nucleic acid amplificationcomprising the steps of: loading a plurality of sample wells with aplurality of biological samples; providing a device configured tothermally cycle a sample block assembly, the sample block assemblycomprising a sample block and a heat sink; placing the loaded pluralityof sample wells onto a sample well receiving region of a sample wellholder; moving the sample well holder and loaded plurality of samplewells into the device until the plurality of sample wells is alignedbetween the sample block assembly positioned beneath the plurality ofsample wells and the sample well holder and a stationary opticaldetection system; moving the sample block assembly from a first positionpermitting the sample well holder to align the plurality of sample wellswith the sample block assembly to a second position permitting thesample block to contact the plurality of sample wells; thermally cyclingthe sample block assembly; and detecting the plurality of biologicalsamples while thermal cycling the sample block assembly.
 2. The methodof claim 1, wherein the step of detecting includes using a CCD camera.3. The method of claim 1, wherein the plurality of sample wells is a96-well sample tray.
 4. The method of claim 1, wherein the plurality ofsample wells is a 384-well sample tray.
 5. The method of claim 1,wherein the plurality of sample wells is a microcard.
 6. A method ofperforming nucleic acid amplification comprising the steps of: loading aplurality of sample wells with a plurality of biological samples;providing a device configured to thermally cycle a sample blockassembly, the thermal block assembly comprising a thermal block and aheat sink; placing the loaded plurality of sample wells onto a samplewell receiving region of a sample well holder; moving the sample wellholder with the loaded plurality of sample wells into the device untilthe plurality of sample wells is aligned between the sample blockassembly positioned beneath the plurality of sample wells and the samplewell holder and a stationary optical detection system; providingmovement between the sample well holder with the plurality of samplewells and the sample block assembly, thereby providing contact betweenthe plurality of sample wells and the sample block assembly; thermallycycling the sample block assembly; and detecting the plurality ofbiological samples while thermal cycling the sample block assembly. 7.The method of claim 6, wherein the optical detection system ispositioned above the sample block assembly.
 8. The method of claim 7,wherein the optical detection system is configured to reducemisalignment of optical components.
 9. The method of claim 7, whereinthe sample well holder and sample wells are dimensioned so that they arecapable of passing between the optical detection system and the sampleblock assembly.
 10. The method of claim 9, wherein the sample wellholder and sample wells are dimensioned so that they are capable ofpassing between the optical detection system and the sample blockassembly without interference.
 11. The method of claim 6, wherein thesample well receiving region is generally rectangular in shape.
 12. Themethod of claim 6, wherein the sample well receiving region supports theplurality of sample wells.
 13. The method of claim 6, wherein theplurality of sample wells is a 96-well sample tray.
 14. The method ofclaim 6, wherein the plurality of sample wells is a 384-well sampletray.
 15. A method of performing nucleic acid amplification comprisingthe steps of: providing a sample well tray comprising of a plurality ofsample wells; loading the sample well tray with a plurality ofbiological samples, wherein the sample well tray has a top surface and abottom surface; providing a device configured to thermally cycle asample block assembly, the sample block assembly comprising a heat sinkand a sample block having a top surface comprising a plurality ofrecesses arranged to correspond to the sample wells of the sample welltray; placing the loaded sample well tray onto a sample well receivingregion of a sample well holder; moving the sample well holder with theloaded sample well tray into the device until the sample well tray isaligned between the plurality of recesses of the sample block positionedbeneath the sample well tray and the sample well holder and a stationaryoptical detection system; contacting the top surface of the sample blockwith the bottom surface of the sample well tray so that the sample wellsare seated against the sample block; thermally cycling the sample block;and detecting the plurality of biological samples while thermal cyclingthe sample block.